MolNFT v1 · #72518 · protein

Basal state form of yeast glycogen synthase

3NAZ · Glycogen [starch] synthase isoform 2: “Basal state form of yeast glycogen synthase”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.76). MolNFT v1 #72518 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3NAZ
Type: protein
Length: 2,459 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycogen [starch] synthase isoform 2; Peptide
EC: 2.4.1.11
UniProt: P27472
Ligands: SO4
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glycogen [starch] synthase isoform 2 (EC 2.4.1.11)	protein	611	49% helix, 15% strand	P27472
C, D	Glycogen [starch] synthase isoform 2 (EC 2.4.1.11)	protein	613	51% helix, 15% strand	P27472
E	Peptide	protein	5	0% helix, 0% strand	—
F	Peptide	protein	6	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 16 copies · chains A, D, B, C, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	993	0.76	0.78	85	SO4
2	919	0.74	0.78	88	SO4
3	858	0.72	0.77	76	SO4
4	785	0.71	0.77	67	SO4
5	471	0.61	0.76	49	empty

Interfaces

8 interfaces between chains.

A–C · 1196 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 1168 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 967 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 906 Å² buried · 6 hydrogen bonds · protein-protein
D–F · 305 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3NAZ · Basal state form of Yeast Glycogen Synthase · the same entry in another collection · chain F against F, TM-score 1.00
P27472 · AlphaFold monomer V2.0 prediction for glycogen [starch] synthase isoform 2 (P27472) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P27472
Elsewhere: RCSB PDB 3NAZ · PDBe 3NAZ · UniProt P27472

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